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    Methods for sequencing with single frequency detection
    1.
    发明授权
    Methods for sequencing with single frequency detection 有权

    公开(公告)号：US11584963B2

    公开(公告)日：2023-02-21

    申请号：US16945173

    申请日：2020-07-31

    Applicant: ULTIMA GENOMICS, INC.

    Inventor： Gilad Almogy ,  Florian Oberstrass

    IPC: C12Q1/6869 ,  C12Q1/6876

    Abstract: The present disclosure provides methods and systems for sequencing nucleic acid molecules using a single frequency during detection, or fewer frequencies than types of nucleotide bases identified during detection. Methods and systems of the present disclosure may involve transiently binding nucleotides. Methods and systems provided herein may enable sequences to be determined at a higher accuracy and efficiency.

    RNA sequencing methods
    3.
    发明授权
    RNA sequencing methods 有权

    公开(公告)号：US11220709B2

    公开(公告)日：2022-01-11

    申请号：US17158953

    申请日：2021-01-26

    Applicant: Ultima Genomics, Inc.

    Inventor： Florian Oberstrass ,  Gilad Almogy

    IPC: C12Q1/6874 ,  C12Q1/6869 ,  C12N15/10

    Abstract: Described herein are methods for determining a sequence of a region of interest from an mRNA molecule. Sequenced polynucleotides can include a barcode region, a homopolymer region (e.g., a poly-A region), and a target region associated with the mRNA molecule. According to some methods, the barcode region omits the same base present in the homopolymer region. According to some methods, extension of the primer used for sequencing is stalled within the homopolymer region. According to some methods, sequencing flow cycles and the different barcode regions of the polynucleotides configured are such that the primer is extended to the end of the barcode region across the plurality of polynucleotides before being extended into the homopolymer region. According to some methods, two primers or a cleavable primer is used to separately sequence the barcode region and the target region.

    RNA sequencing methods
    4.
    发明授权
    RNA sequencing methods 有权

    公开(公告)号：US11578363B2

    公开(公告)日：2023-02-14

    申请号：US16925778

    申请日：2020-07-10

    Applicant: Ultima Genomics, Inc.

    Inventor： Florian Oberstrass ,  Gilad Almogy

    IPC: C12Q1/6869 ,  C12N15/10 ,  C12Q1/6874

    Abstract: Described herein are methods for determining a sequence of a region of interest from an mRNA molecule. Sequenced polynucleotides can include a barcode region, a homopolymer region (e.g., a poly-A region), and a target region associated with the mRNA molecule. According to some methods, the barcode region omits the same base present in the homopolymer region. According to some methods, extension of the primer used for sequencing is stalled within the homopolymer region. According to some methods, sequencing flow cycles and the different barcode regions of the polynucleotides configured are such that the primer is extended to the end of the barcode region across the plurality of polynucleotides before being extended into the homopolymer region. According to some methods, two primers or a cleavable primer is used to separately sequence the barcode region and the target region.

    ACCELERATED SEQUENCING METHODS
    7.
    发明申请
    ACCELERATED SEQUENCING METHODS 有权

    公开(公告)号：US20230060685A1

    公开(公告)日：2023-03-02

    申请号：US17822760

    申请日：2022-08-26

    Applicant: Ultima Genomics, Inc.

    Inventor： Mark Pratt ,  Gilad Almogy ,  Dumitru Brinza ,  Eliane Trepagnier ,  Omer Barad ,  Yoav Etzioni ,  Florian Oberstrass

    IPC: C12Q1/6869 ,  G16B30/00 ,  C12Q1/6827

    Abstract: Described herein are methods of generating a coupled sequencing read pair for a polynucleotide, and methods of analyzing the coupled sequencing read pair. The coupled sequencing read pair can be analyzed to detect polynucleotide variants, including at loci that are not directly sequenced within the coupled sequencing read pair. Other analytical methods can include using coupled sequencing read pairs to construct or validate a consensus sequence. The coupled sequencing read pair may be generated for a polynucleotide by generating sequencing data for a first region by extending a primer using labeled nucleotides; further extending the primer through a second region using nucleotides provided in a second region flow order, wherein primer extension through the second region is faster than primer extension through the first region; and generating sequencing data associated with a sequence of a third region of the polynucleotide by further extending the primer using labeled nucleotides.

    RNA sequencing methods
    8.
    发明授权
    RNA sequencing methods 有权

    公开(公告)号：US11220710B2

    公开(公告)日：2022-01-11

    申请号：US17158960

    申请日：2021-01-26

    Applicant: Ultima Genomics, Inc.

    Inventor： Florian Oberstrass ,  Gilad Almogy

    IPC: C12Q1/6869 ,  C12Q1/6874 ,  C12N15/10

    Abstract: Described herein are methods for determining a sequence of a region of interest from an mRNA molecule. Sequenced polynucleotides can include a barcode region, a homopolymer region (e.g., a poly-A region), and a target region associated with the mRNA molecule. According to some methods, the barcode region omits the same base present in the homopolymer region. According to some methods, extension of the primer used for sequencing is stalled within the homopolymer region. According to some methods, sequencing flow cycles and the different barcode regions of the polynucleotides configured are such that the primer is extended to the end of the barcode region across the plurality of polynucleotides before being extended into the homopolymer region. According to some methods, two primers or a cleavable primer is used to separately sequence the barcode region and the target region.

    Methods for nucleic acid analysis
    9.
    发明授权
    Methods for nucleic acid analysis 有权

    公开(公告)号：US11891658B2

    公开(公告)日：2024-02-06

    申请号：US17394692

    申请日：2021-08-05

    Applicant: Ultima Genomics, Inc.

    Inventor： Gilad Almogy ,  Florian Oberstrass ,  Omer Barad ,  Chandan Shee

    IPC: C12Q1/686

    CPC classification number: C12Q1/686 ,  C12Q2563/107 ,  C12Q2563/149 ,  C12Q2563/159

    Abstract: The present disclosure provides methods and processes for increasing the efficiency and accuracy of nucleic acid sequencing using techniques such as polymerase chain reaction (PCR). The methods described herein can be used to achieve clonal amplification even with a greater than Poisson distribution of beads and/or nucleic acid templates into an emulsion. A PCR method may comprise generating a partition (e.g., a droplet) comprising at least two beads and/or at least two nucleic acid molecules and generating clonal amplification products corresponding to the nucleic acid molecule, at least a subset of which may be attached to a bead.

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